[BioRuby-cvs] bioruby/lib/bio/appl/hmmer report.rb,1.5,1.6

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/hmmer
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/appl/hmmer

Modified Files:
	report.rb 
Log Message:
* expanded tab at the line head


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/hmmer/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb	9 Aug 2005 09:58:19 -0000	1.5
--- report.rb	8 Sep 2005 01:22:09 -0000	1.6
***************
*** 33,42 ****
          @query_info =parse_query_info($3)
  
! 	case @program['name']
! 	when /hmmsearch/
! 	  is_hmmsearch = true
! 	else
! 	  is_hmmsearch = false		# hmmpfam
! 	end
  
          # Scores for complete sequences. (parsed to Hit objects)
--- 33,42 ----
          @query_info =parse_query_info($3)
  
!         case @program['name']
!         when /hmmsearch/
!           is_hmmsearch = true
!         else
!           is_hmmsearch = false		# hmmpfam
!         end
  
          # Scores for complete sequences. (parsed to Hit objects)
***************
*** 62,67 ****
          $1.split(/^\S+.*?\n/).slice(1..-1).each_with_index do |al,k|
            al2 = al.gsub(/\n\n/,"\n").to_s.collect { |l|
! 	    l.sub(/^.{19}/,'').sub(/\s(\d+|-)\s*$/,'')
! 	  }
            align = ['', '', '']
            al2.each_with_index { |s,i| align[i%3] += s.chomp }
--- 62,67 ----
          $1.split(/^\S+.*?\n/).slice(1..-1).each_with_index do |al,k|
            al2 = al.gsub(/\n\n/,"\n").to_s.collect { |l|
!             l.sub(/^.{19}/,'').sub(/\s(\d+|-)\s*$/,'')
!           }
            align = ['', '', '']
            al2.each_with_index { |s,i| align[i%3] += s.chomp }
***************
*** 108,118 ****
        end
        attr_reader :program, :parameter, :query_info, :hits,
! 	:histogram, :statistical_detail, :total_seq_searched,
! 	:whole_seq_top_hits, :domain_top_hits 
  
        def each
! 	@hits.each do |x|
! 	  yield x
! 	end
        end
  
--- 108,118 ----
        end
        attr_reader :program, :parameter, :query_info, :hits,
!         :histogram, :statistical_detail, :total_seq_searched,
!         :whole_seq_top_hits, :domain_top_hits 
  
        def each
!         @hits.each do |x|
!           yield x
!         end
        end
  
***************
*** 122,127 ****
            @is_hmmsearch = is_hmmsearch
  
! 	  @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,
! 	    score, evalue = data.split(' ')
            @seq_f = seq_f.to_i
            @seq_t = seq_t.to_i
--- 122,127 ----
            @is_hmmsearch = is_hmmsearch
  
!           @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,
!             score, evalue = data.split(' ')
            @seq_f = seq_f.to_i
            @seq_t = seq_t.to_i
***************
*** 137,142 ****
          end
          attr_accessor :accession, :domain, :seq_f, :seq_t, :seq_ft,
! 	  :hmm_f, :hmm_t, :hmm_ft, :score, :evalue, :midline, :hmmseq,
! 	  :flatseq, :query_frame, :target_frame
  
          def query_seq
--- 137,142 ----
          end
          attr_accessor :accession, :domain, :seq_f, :seq_t, :seq_ft,
!           :hmm_f, :hmm_t, :hmm_ft, :score, :evalue, :midline, :hmmseq,
!           :flatseq, :query_frame, :target_frame
  
          def query_seq
***************
*** 174,178 ****
            if /^(\S+)\s+(.*)\s+(\S+)\s+(\S+)\s+(\S+)$/ =~ data
              @accession, @description, @score, @evalue, @num = 
! 	      [$1, $2, $3.to_f, $4.to_f, $5.to_i]
            end
          end
--- 174,178 ----
            if /^(\S+)\s+(.*)\s+(\S+)\s+(\S+)\s+(\S+)$/ =~ data
              @accession, @description, @score, @evalue, @num = 
!               [$1, $2, $3.to_f, $4.to_f, $5.to_i]
            end
          end
***************
*** 206,210 ****
          hash = {}
          hash['name'], hash['version'], hash['copyright'], hash['license'] =
! 	  data.split(/\n/)
          hash
        end
--- 206,210 ----
          hash = {}
          hash['name'], hash['version'], hash['copyright'], hash['license'] =
!           data.split(/\n/)
          hash
        end